Merge branch 'master' of https://github.com/HBClab/accelBIDSTransform into fix_singularity

Author: jdkent

accel_code/excel_lookup.py

@@ -14,7 +14,7 @@ def excel_lookup(lab_id, date, excel_file):
     df.LabID = df.LabID.astype(str)
 
     try:
-        ses = df[(df['LabID'].str.contains(lab_id)) &
+        ses = df[(df['LabID'].str.contains(str(lab_id))) &
                  (df['File date'] == date)]
 
         # Check to make sure no labid/date combo gives more than one result

accel_code/run.py

@@ -42,7 +42,7 @@ def main():
     lab_id = utils.get_lab_id(opts.old_file_path)
     date = utils.get_date(opts.old_file_path)
 
-    ses_id, project = excel_lookup.excel_lookup(lab_id, date, opts.excel_file)
+    ses_id, project = excel_lookup.excel_lookup(lab_id, date, opts.excel_file_path)
 
     sub_id = redcap_query.redcap_query(lab_id, project, opts.api_key)
 

accel_code/utils.py

@@ -103,7 +103,7 @@ def get_date(old_file_path):
 # This function extracts the lab id from the old accelerometer file name
 def get_lab_id(old_file_path):
     old_file_name = os.path.basename(old_file_path)
-    return(old_file_name.split(' ')[0])
+    return(int(old_file_name.split(' ')[0]))
 
 
 # This function returns the root data path for storing project data
@@ -164,4 +164,5 @@ def make_directory(old_path, new_path, replace):
             os.remove(new_path)
             copyfile(old_path, new_path)
     else:
+        os.makedirs(os.path.dirname(new_path), exist_ok=True)
         copyfile(old_path, new_path)